7-104242816-A-G

Variant names:

• chr7-104242816-A-G
• rs1557664

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 0.177 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.177 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

Gnomad4 AFR AF: 0.0498

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.199

Alfa AF: 0.194 Hom.: 1876

Bravo AF: 0.168

Asia WGS AF: 0.222 AC: 770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1557664; hg19: chr7-103883264;