rs4418214

Variant names:

• chr6-31423624-T-C
• rs4418214
• ENST00000673857.1:n.62+22861T>C

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.62+22861T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0769 in 151,934 control chromosomes in the GnomAD database, including 498 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 0.077 (498 hom., cov: 32)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 47 publications found

Genes affected

ENSG00000288587 (HGNC:):

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 = 0.0842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288587	ENST00000673857.1	n.62+22861T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0769 AC: 11673 AN: 151816 Hom.: 499 Cov.: 32

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.0473

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.0640

Gnomad SAS AF: 0.0802

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0860

Gnomad OTH AF: 0.0629

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

GnomAD4 genome AF: 0.0769 AC: 11679 AN: 151934 Hom.: 498 Cov.: 32 AF XY: 0.0772 AC XY: 5734 AN XY: 74292

African (AFR) AF: 0.0697 AC: 2883 AN: 41364

American (AMR) AF: 0.0473 AC: 719 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.0594 AC: 206 AN: 3466

East Asian (EAS) AF: 0.0638 AC: 330 AN: 5172

South Asian (SAS) AF: 0.0795 AC: 383 AN: 4820

European-Finnish (FIN) AF: 0.0889 AC: 942 AN: 10600

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0860 AC: 5850 AN: 67990

Other (OTH) AF: 0.0632 AC: 133 AN: 2106

Alfa AF: 0.0771 Hom.: 1007

Bravo AF: 0.0741

Asia WGS AF: 0.0850 AC: 293 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.43
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs4418214; hg19: chr6-31391401;