chr7-127632346-A-G

Position:

• chr7-127632346-A-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 0.194 in 152,094 control chromosomes in the GnomAD database, including 3,038 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 0.19 (3038 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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: 0.194 AC: 29489 AN: 151976 Hom.: 3038 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.194 AC: 29502 AN: 152094 Hom.: 3038 Cov.: 31 AF XY: 0.194 AC XY: 14436 AN XY: 74364

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.177

Alfa AF: 0.181 Hom.: 1537

Bravo AF: 0.194

Asia WGS AF: 0.166 AC: 579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.5
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1440971; hg19: chr7-127272400;