rs970741

Positions:

• chr1-169510807-T-C

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 0.256 in 151,710 control chromosomes in the GnomAD database, including 5,099 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 0.26 (5099 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38808 AN: 151592 Hom.: 5090 Cov.: 31

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.256 AC: 38830 AN: 151710 Hom.: 5099 Cov.: 31 AF XY: 0.257 AC XY: 19033 AN XY: 74144

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.267

Alfa AF: 0.271 Hom.: 2660

Bravo AF: 0.266

Asia WGS AF: 0.283 AC: 982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs970741; hg19: chr1-169480045;