rs1960773

Positions:

• chr4-68671436-A-C
• chr4-68671436-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.537 in 146,526 control chromosomes in the GnomAD database, including 21,553 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 0.54 (21553 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

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: 0.537 AC: 78655 AN: 146414 Hom.: 21510 Cov.: 25

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.537 AC: 78756 AN: 146526 Hom.: 21553 Cov.: 25 AF XY: 0.540 AC XY: 38509 AN XY: 71354

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.534

Alfa AF: 0.378 Hom.: 847

Bravo AF: 0.545

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1960773; hg19: chr4-69537154;