7-104242816-A-G

Variant names:

• chr7-104242816-A-G
• rs1557664

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 0.177 in 152,056 control chromosomes in the GnomAD database, including 2,947 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 0.18 (2947 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.47
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26901 AN: 151940 Hom.: 2947 Cov.: 32

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.177 AC: 26896 AN: 152056 Hom.: 2947 Cov.: 32 AF XY: 0.180 AC XY: 13394 AN XY: 74316

African (AFR) AF: 0.0498 AC: 2069 AN: 41524

American (AMR) AF: 0.185 AC: 2826 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 732 AN: 3472

East Asian (EAS) AF: 0.257 AC: 1322 AN: 5150

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4810

European-Finnish (FIN) AF: 0.265 AC: 2799 AN: 10572

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15369 AN: 67942

Other (OTH) AF: 0.199 AC: 421 AN: 2112

Alfa AF: 0.198 Hom.: 2566

Bravo AF: 0.168

Asia WGS AF: 0.222 AC: 770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.75
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs1557664; hg19: chr7-103883264;