rs9729377

Variant names:

• chr1-84810967-T-C
• rs9729377

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 0.368 in 152,060 control chromosomes in the GnomAD database, including 11,291 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 0.37 (11291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 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: 0.368 AC: 55907 AN: 151942 Hom.: 11280 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.368 AC: 55953 AN: 152060 Hom.: 11291 Cov.: 32 AF XY: 0.359 AC XY: 26683 AN XY: 74338

African (AFR) AF: 0.523 AC: 21688 AN: 41464

American (AMR) AF: 0.283 AC: 4319 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1335 AN: 3472

East Asian (EAS) AF: 0.00444 AC: 23 AN: 5176

South Asian (SAS) AF: 0.279 AC: 1344 AN: 4810

European-Finnish (FIN) AF: 0.262 AC: 2767 AN: 10574

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23269 AN: 67972

Other (OTH) AF: 0.361 AC: 764 AN: 2114

Alfa AF: 0.362 Hom.: 20099

Bravo AF: 0.376

Asia WGS AF: 0.178 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.48
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs9729377; hg19: chr1-85276650;