chr10-37871571-C-T

Variant names:

• chr10-37871571-C-T
• rs1208611

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 0.0678 in 152,142 control chromosomes in the GnomAD database, including 391 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 0.068 (391 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.088 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: 0.0678 AC: 10314 AN: 152022 Hom.: 390 Cov.: 32

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0662

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00850

Gnomad FIN AF: 0.0714

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0898

Gnomad OTH AF: 0.0792

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

GnomAD4 genome AF: 0.0678 AC: 10316 AN: 152142 Hom.: 391 Cov.: 32 AF XY: 0.0650 AC XY: 4832 AN XY: 74370

Gnomad4 AFR AF: 0.0429

Gnomad4 AMR AF: 0.0661

Gnomad4 ASJ AF: 0.0847

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00851

Gnomad4 FIN AF: 0.0714

Gnomad4 NFE AF: 0.0899

Gnomad4 OTH AF: 0.0783

Alfa AF: 0.0584 Hom.: 65

Bravo AF: 0.0677

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1208611; hg19: chr10-38160499;