chr7-64357798-T-G

Variant names:

• chr7-64357798-T-G
• rs621054

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 0.487 in 82,416 control chromosomes in the GnomAD database, including 6,355 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 0.49 (6355 hom., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.537 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: 0.487 AC: 40162 AN: 82384 Hom.: 6351 Cov.: 21

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.487 AC: 40168 AN: 82416 Hom.: 6355 Cov.: 21 AF XY: 0.482 AC XY: 19518 AN XY: 40464

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.523

Alfa AF: 0.304 Hom.: 967

Bravo AF: 0.253

Asia WGS AF: 0.281 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.3
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs621054; hg19: chr7-63818176;