chr7-104042236-G-C

Variant names:

• chr7-104042236-G-C
• rs10256829

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.719 AC: 29788 AN: 41436

American (AMR) AF: 0.371 AC: 5662 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3468

East Asian (EAS) AF: 0.526 AC: 2723 AN: 5172

South Asian (SAS) AF: 0.361 AC: 1739 AN: 4814

European-Finnish (FIN) AF: 0.119 AC: 1261 AN: 10588

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.0862 AC: 5861 AN: 67964

Other (OTH) AF: 0.267 AC: 563 AN: 2112

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
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs10256829; hg19: chr7-103682683;