rs7206971

chr17-47347749-G-Achr17-47347749-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152347.5(EFCAB13):c.518-59G>A variant causes a intron 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_152347.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFCAB13	NM_152347.5	c.518-59G>A		intron_variant		ENST00000331493.7
EFCAB13	NM_001195192.2	c.517+2651G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFCAB13	ENST00000331493.7	c.518-59G>A		intron_variant		1	NM_152347.5	A2
EFCAB13	ENST00000517310.5	c.73+2651G>A		intron_variant		2
EFCAB13	ENST00000517484.5	c.517+2651G>A		intron_variant		2		P2
EFCAB13	ENST00000520776.5	n.651+2651G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR exome AF: 0.462

Gnomad4 AMR exome AF: 0.334

Gnomad4 ASJ exome AF: 0.432

Gnomad4 EAS exome AF: 0.272

Gnomad4 SAS exome AF: 0.415

Gnomad4 FIN exome AF: 0.483

Gnomad4 NFE exome AF: 0.488

Gnomad4 OTH exome AF: 0.467

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

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.458

Alfa AF: 0.481 Hom.: 13774

Bravo AF: 0.457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.18
Dann	Benign	0.38

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

Publications

LitVar

Other links and lift over

dbSNP: rs7206971; hg19: chr17-45425115;