rs1860148

Positions:

• chr7-76377497-T-A
• chr7-76377497-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 0.172 in 152,236 control chromosomes in the GnomAD database, including 2,809 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 0.17 (2809 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

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 (EAS) allele frequency at 95% confidence interval = 0.303 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: 0.172 AC: 26236 AN: 152118 Hom.: 2808 Cov.: 32

Gnomad AFR AF: 0.0602

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.172 AC: 26238 AN: 152236 Hom.: 2809 Cov.: 32 AF XY: 0.173 AC XY: 12904 AN XY: 74444

Gnomad4 AFR AF: 0.0601

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.173

Alfa AF: 0.0957 Hom.: 151

Bravo AF: 0.172

Asia WGS AF: 0.276 AC: 957 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	7.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1860148; hg19: chr7-76006814;