1-96698787-A-G

Variant names:

• chr1-96698787-A-G
• rs7544736

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 0.223 in 151,878 control chromosomes in the GnomAD database, including 4,202 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 0.22 (4202 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33772 AN: 151760 Hom.: 4193 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.223 AC: 33794 AN: 151878 Hom.: 4202 Cov.: 32 AF XY: 0.221 AC XY: 16441 AN XY: 74226

African (AFR) AF: 0.337 AC: 13950 AN: 41370

American (AMR) AF: 0.157 AC: 2391 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1087 AN: 5176

South Asian (SAS) AF: 0.170 AC: 818 AN: 4816

European-Finnish (FIN) AF: 0.195 AC: 2053 AN: 10532

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12017 AN: 67958

Other (OTH) AF: 0.216 AC: 454 AN: 2106

Alfa AF: 0.194 Hom.: 11575

Bravo AF: 0.224

Asia WGS AF: 0.187 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.94
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7544736; hg19: chr1-97164343;