17-47347749-G-A

Variant names:

• chr17-47347749-G-A
• rs7206971
• NM_152347.5:c.518-59G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001426591.1(EFCAB13):​c.*2634G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 1,242,976 control chromosomes in the GnomAD database, including 141,622 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.47 (16827 hom., cov: 32)
  • Exomes 𝑓: 0.47 (124795 hom.)
• Consequence: EFCAB13 NM_001426591.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 82 publications found

Genes affected

EFCAB13 (HGNC:26864): (EF-hand calcium binding domain 13)

EFCAB13-DT (HGNC:55338): (EFCAB13 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001426591.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB13	NM_152347.5	MANE Select	c.518-59G>A		intron	N/A	NP_689560.3
	EFCAB13	NM_001426591.1		c.*2634G>A		3_prime_UTR	Exon 8 of 8	NP_001413520.1
	EFCAB13	NM_001426592.1		c.*2634G>A		3_prime_UTR	Exon 7 of 7	NP_001413521.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB13	ENST00000331493.7	TSL:1 MANE Select	c.518-59G>A		intron	N/A	ENSP00000332111.2	Q8IY85-1
	EFCAB13	ENST00000517484.5	TSL:2	c.517+2651G>A		intron	N/A	ENSP00000430048.1	Q8IY85-2
	EFCAB13	ENST00000517310.5	TSL:2	c.73+2651G>A		intron	N/A	ENSP00000466136.1	K7ELL9

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70806 AN: 151942 Hom.: 16822 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.460

GnomAD4 exome AF: 0.475 AC: 517744 AN: 1090916 Hom.: 124795 AF XY: 0.475 AC XY: 250760 AN XY: 527942

African (AFR) AF: 0.462 AC: 10859 AN: 23500

American (AMR) AF: 0.334 AC: 6544 AN: 19590

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 7218 AN: 16708

East Asian (EAS) AF: 0.272 AC: 8299 AN: 30504

South Asian (SAS) AF: 0.415 AC: 12171 AN: 29300

European-Finnish (FIN) AF: 0.483 AC: 18545 AN: 38424

Middle Eastern (MID) AF: 0.396 AC: 1632 AN: 4124

European-Non Finnish (NFE) AF: 0.488 AC: 431833 AN: 884538

Other (OTH) AF: 0.467 AC: 20643 AN: 44228

GnomAD4 genome AF: 0.466 AC: 70845 AN: 152060 Hom.: 16827 Cov.: 32 AF XY: 0.462 AC XY: 34322 AN XY: 74344

African (AFR) AF: 0.476 AC: 19763 AN: 41478

American (AMR) AF: 0.383 AC: 5847 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1615 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1313 AN: 5188

South Asian (SAS) AF: 0.418 AC: 2015 AN: 4826

European-Finnish (FIN) AF: 0.493 AC: 5203 AN: 10562

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33561 AN: 67952

Other (OTH) AF: 0.458 AC: 965 AN: 2108

Alfa AF: 0.481 Hom.: 20143

Bravo AF: 0.457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.18
DANN	Benign	0.38
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7206971; hg19: chr17-45425115;