rs1163091

Positions:

• chr4-49569822-C-G
• chr4-49569822-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0127 in 137,864 control chromosomes in the GnomAD database, including 7 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 0.013 (7 hom., cov: 51)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.87

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0127 (1757/137864) while in subpopulation AFR AF= 0.0476 (1651/34704). AF 95% confidence interval is 0.0457. There are 7 homozygotes in gnomad4. There are 813 alleles in male gnomad4 subpopulation. Median coverage is 51. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0127 AC: 1749 AN: 137816 Hom.: 6 Cov.: 51

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00561

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000969

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00787

Gnomad NFE AF: 0.000166

Gnomad OTH AF: 0.00839

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

GnomAD4 genome AF: 0.0127 AC: 1757 AN: 137864 Hom.: 7 Cov.: 51 AF XY: 0.0122 AC XY: 813 AN XY: 66390

Gnomad4 AFR AF: 0.0476

Gnomad4 AMR AF: 0.00561

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000971

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000166

Gnomad4 OTH AF: 0.00832

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	9.5
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1163091; hg19: chr4-49571839;