rs1860797

Variant names:

• chr7-31297374-T-C
• rs1860797

Your query was ambiguous. Multiple possible variants found:

• chr7-31297374-T-C
• chr7-31297374-T-G

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 0.0683 in 152,274 control chromosomes in the GnomAD database, including 562 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 (562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 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: 0.0681 AC: 10362 AN: 152156 Hom.: 547 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0439

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.0366

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0683 AC: 10406 AN: 152274 Hom.: 562 Cov.: 32 AF XY: 0.0669 AC XY: 4984 AN XY: 74468

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.0439

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0577

Gnomad4 FIN AF: 0.0366

Gnomad4 NFE AF: 0.0340

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0163 Hom.: 5

Bravo AF: 0.0701

Asia WGS AF: 0.0380 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
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: rs1860797; hg19: chr7-31336988;