7-104042236-G-C

Position:

• chr7-104042236-G-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 0.317 in 152,018 control chromosomes in the GnomAD database, including 13,462 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 0.32 (13462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 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: 0.317 AC: 48101 AN: 151900 Hom.: 13419 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.0862

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.317 AC: 48203 AN: 152018 Hom.: 13462 Cov.: 32 AF XY: 0.320 AC XY: 23819 AN XY: 74350

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0862

Gnomad4 OTH AF: 0.267

Alfa AF: 0.216 Hom.: 996

Bravo AF: 0.354

Asia WGS AF: 0.431 AC: 1497 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10256829; hg19: chr7-103682683;