chr17-62384289-A-T

Variant names:

• chr17-62384289-A-T
• rs2009866
• NM_173503.4:c.74+1236A>T

Variant summary

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

The NM_173503.4(EFCAB3):​c.74+1236A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,154 control chromosomes in the GnomAD database, including 42,162 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 0.71 (42162 hom., cov: 32)
• Consequence: EFCAB3 NM_173503.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677
• Publications: 3 publications found

Genes affected

EFCAB3 (HGNC:26379): (EF-hand calcium binding domain 3) Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB3	NM_173503.4	c.74+1236A>T		intron_variant	Intron 2 of 9	ENST00000305286.8	NP_775774.1
EFCAB3	NM_001144933.2	c.230+1236A>T		intron_variant	Intron 4 of 11		NP_001138405.1
EFCAB3	XM_011524381.3	c.140+1236A>T		intron_variant	Intron 2 of 9		XP_011522683.2
EFCAB3	XM_011524380.2	c.74+1236A>T		intron_variant	Intron 2 of 9		XP_011522682.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFCAB3	ENST00000305286.8	c.74+1236A>T		intron_variant	Intron 2 of 9	1	NM_173503.4	ENSP00000302649.3

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107415 AN: 152036 Hom.: 42153 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.706 AC: 107446 AN: 152154 Hom.: 42162 Cov.: 32 AF XY: 0.708 AC XY: 52648 AN XY: 74382

African (AFR) AF: 0.347 AC: 14413 AN: 41486

American (AMR) AF: 0.796 AC: 12160 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3025 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2771 AN: 5160

South Asian (SAS) AF: 0.690 AC: 3324 AN: 4816

European-Finnish (FIN) AF: 0.910 AC: 9648 AN: 10602

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59465 AN: 68018

Other (OTH) AF: 0.744 AC: 1574 AN: 2116

Alfa AF: 0.778 Hom.: 6045

Bravo AF: 0.685

Asia WGS AF: 0.612 AC: 2133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.5
DANN	Benign	0.77
PhyloP100		-0.68
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: rs2009866; hg19: chr17-60461650;