rs997649

Variant names:

• chr6-78488425-T-G
• rs997649

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 0.0267 in 152,214 control chromosomes in the GnomAD database, including 93 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 0.027 (93 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.119 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: 0.0267 AC: 4065 AN: 152096 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.00526

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0317

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0267 AC: 4069 AN: 152214 Hom.: 93 Cov.: 32 AF XY: 0.0290 AC XY: 2160 AN XY: 74452

Gnomad4 AFR AF: 0.00525

Gnomad4 AMR AF: 0.0374

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0227

Gnomad4 NFE AF: 0.0318

Gnomad4 OTH AF: 0.0308

Alfa AF: 0.0282 Hom.: 10

Bravo AF: 0.0236

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.3
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs997649; hg19: chr6-79198142;