rs4350617

Positions:

• chr17-30096070-G-A
• chr17-30096070-G-C
• chr17-30096070-G-T

Variant summary

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

The NM_198529.4(EFCAB5):​c.4321+3134G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,022 control chromosomes in the GnomAD database, including 13,721 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 0.38 (13721 hom., cov: 31)
• Consequence: EFCAB5 NM_198529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568

Genes affected

EFCAB5 (HGNC:24801): (EF-hand calcium binding domain 5) Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000265394 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFCAB5	NM_198529.4	c.4321+3134G>A		intron_variant		ENST00000394835.8	NP_940931.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFCAB5	ENST00000394835.8	c.4321+3134G>A		intron_variant		1	NM_198529.4	ENSP00000378312.3
EFCAB5	ENST00000588978.1	c.2132-11764G>A		intron_variant		1		ENSP00000465109.1
EFCAB5	ENST00000419434.5	c.3367+3134G>A		intron_variant		2		ENSP00000417009.1
ENSG00000265394	ENST00000582938.1	n.107-5426C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58340 AN: 151904 Hom.: 13724 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.425

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.384 AC: 58326 AN: 152022 Hom.: 13721 Cov.: 31 AF XY: 0.393 AC XY: 29202 AN XY: 74294

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.422

Alfa AF: 0.419 Hom.: 6610

Bravo AF: 0.380

Asia WGS AF: 0.574 AC: 1997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.8
DANN	Benign	0.87

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: rs4350617; hg19: chr17-28423088;