rs2105902

Variant names:

• chr6-32427921-A-T
• rs2105902
• ENST00000766247.1:n.283-6171A>T

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.283-6171A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0918 in 152,136 control chromosomes in the GnomAD database, including 930 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 0.092 (930 hom., cov: 32)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 11 publications found

Genes affected

ENSG00000299769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 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
ENSG00000299769	ENST00000766247.1	n.283-6171A>T		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1	n.391+2449A>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0919 AC: 13967 AN: 152018 Hom.: 931 Cov.: 32

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0826

Gnomad ASJ AF: 0.0711

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.00394

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.0784

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

GnomAD4 genome AF: 0.0918 AC: 13961 AN: 152136 Hom.: 930 Cov.: 32 AF XY: 0.0876 AC XY: 6520 AN XY: 74398

African (AFR) AF: 0.0230 AC: 954 AN: 41530

American (AMR) AF: 0.0823 AC: 1258 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0711 AC: 246 AN: 3462

East Asian (EAS) AF: 0.0162 AC: 84 AN: 5186

South Asian (SAS) AF: 0.00394 AC: 19 AN: 4824

European-Finnish (FIN) AF: 0.140 AC: 1473 AN: 10558

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9660 AN: 67990

Other (OTH) AF: 0.0775 AC: 163 AN: 2102

Alfa AF: 0.118 Hom.: 162

Bravo AF: 0.0860

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.68
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2105902; hg19: chr6-32395698; COSMIC: COSV67970822;