chr6-19879337-C-T

Variant names:

• chr6-19879337-C-T
• rs7772056

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 0.43 in 152,036 control chromosomes in the GnomAD database, including 14,447 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 0.43 (14447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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: 0.430 AC: 65283 AN: 151922 Hom.: 14412 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.430 AC: 65365 AN: 152036 Hom.: 14447 Cov.: 32 AF XY: 0.434 AC XY: 32228 AN XY: 74322

African (AFR) AF: 0.509 AC: 21095 AN: 41454

American (AMR) AF: 0.484 AC: 7386 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1331 AN: 3472

East Asian (EAS) AF: 0.428 AC: 2209 AN: 5166

South Asian (SAS) AF: 0.349 AC: 1685 AN: 4828

European-Finnish (FIN) AF: 0.484 AC: 5101 AN: 10544

Middle Eastern (MID) AF: 0.390 AC: 113 AN: 290

European-Non Finnish (NFE) AF: 0.373 AC: 25364 AN: 67984

Other (OTH) AF: 0.406 AC: 858 AN: 2112

Alfa AF: 0.394 Hom.: 19585

Bravo AF: 0.438

Asia WGS AF: 0.442 AC: 1532 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.29
DANN	Benign	0.39
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs7772056; hg19: chr6-19879568;