4-122602720-G-T

Variant names:

• chr4-122602720-G-T
• rs7682241
• ENST00000776599.1:n.242C>A

Variant summary

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

The ENST00000776599.1(ENSG00000301148):​n.242C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,988 control chromosomes in the GnomAD database, including 7,985 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 0.31 (7985 hom., cov: 32)
• Consequence: ENSG00000301148 ENST00000776599.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491
• Publications: 26 publications found

Genes affected

ENSG00000301148 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.506 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
ENSG00000301148	ENST00000776599.1	n.242C>A		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000301148	ENST00000776601.1	n.282C>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000301148	ENST00000776602.1	n.362C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46935 AN: 151868 Hom.: 7978 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.309 AC: 46959 AN: 151988 Hom.: 7985 Cov.: 32 AF XY: 0.315 AC XY: 23425 AN XY: 74280

African (AFR) AF: 0.161 AC: 6693 AN: 41478

American (AMR) AF: 0.396 AC: 6040 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3464

East Asian (EAS) AF: 0.380 AC: 1962 AN: 5162

South Asian (SAS) AF: 0.523 AC: 2513 AN: 4804

European-Finnish (FIN) AF: 0.354 AC: 3735 AN: 10548

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.344 AC: 23375 AN: 67960

Other (OTH) AF: 0.349 AC: 735 AN: 2108

Alfa AF: 0.337 Hom.: 27803

Bravo AF: 0.304

Asia WGS AF: 0.437 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.0
DANN	Benign	0.62
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs7682241; hg19: chr4-123523875;