rs997649

chr6-78488425-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;