1-102737551-T-C

Position:

• chr1-102737551-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 0.608 in 151,498 control chromosomes in the GnomAD database, including 30,799 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 0.61 (30799 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.666

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.728 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: 0.609 AC: 92141 AN: 151380 Hom.: 30794 Cov.: 29

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.608 AC: 92171 AN: 151498 Hom.: 30799 Cov.: 29 AF XY: 0.615 AC XY: 45520 AN XY: 73996

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.624

Alfa AF: 0.703 Hom.: 41231

Bravo AF: 0.590

Asia WGS AF: 0.623 AC: 2160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1376359; hg19: chr1-103203107;