rs7990965

Variant names:

• chr13-72044157-T-C
• rs7990965

Variant summary

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

The variant allele was found at a frequency of 0.049 in 152,312 control chromosomes in the GnomAD database, including 352 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 0.049 (352 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.137 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

Frequencies

GnomAD3 genomes AF: 0.0489 AC: 7442 AN: 152194 Hom.: 348 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0207

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.00781

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0184

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0490 AC: 7465 AN: 152312 Hom.: 352 Cov.: 32 AF XY: 0.0498 AC XY: 3706 AN XY: 74470

African (AFR) AF: 0.101 AC: 4180 AN: 41564

American (AMR) AF: 0.0207 AC: 316 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3470

East Asian (EAS) AF: 0.141 AC: 731 AN: 5178

South Asian (SAS) AF: 0.146 AC: 706 AN: 4824

European-Finnish (FIN) AF: 0.00781 AC: 83 AN: 10624

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

European-Non Finnish (NFE) AF: 0.0184 AC: 1250 AN: 68042

Other (OTH) AF: 0.0473 AC: 100 AN: 2112

Alfa AF: 0.0303 Hom.: 460

Bravo AF: 0.0492

Asia WGS AF: 0.165 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	4.9
DANN	Benign	0.58
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7990965; hg19: chr13-72618295;