rs767055

Variant names:

• chr21-22961300-G-A
• rs767055
• ENST00000764465.1:n.297+4942C>T

Variant summary

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

The ENST00000764465.1(ENSG00000299538):​n.297+4942C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 152,076 control chromosomes in the GnomAD database, including 29,814 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 0.63 (29814 hom., cov: 33)
• Consequence: ENSG00000299538 ENST00000764465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 4 publications found

Genes affected

ENSG00000299538 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.663 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
ENSG00000299538	ENST00000764465.1	n.297+4942C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95317 AN: 151958 Hom.: 29787 Cov.: 33

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.627 AC: 95396 AN: 152076 Hom.: 29814 Cov.: 33 AF XY: 0.626 AC XY: 46530 AN XY: 74324

African (AFR) AF: 0.626 AC: 25945 AN: 41476

American (AMR) AF: 0.622 AC: 9490 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2369 AN: 3472

East Asian (EAS) AF: 0.609 AC: 3144 AN: 5162

South Asian (SAS) AF: 0.682 AC: 3287 AN: 4820

European-Finnish (FIN) AF: 0.610 AC: 6452 AN: 10584

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42518 AN: 67974

Other (OTH) AF: 0.641 AC: 1356 AN: 2114

Alfa AF: 0.629 Hom.: 60933

Bravo AF: 0.628

Asia WGS AF: 0.651 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.67
DANN	Benign	0.52
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs767055; hg19: chr21-24333621;