chr6-160314714-T-G

Variant names:

• chr6-160314714-T-G
• rs410569

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 0.617 in 152,088 control chromosomes in the GnomAD database, including 29,230 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 0.62 (29230 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 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: 0.617 AC: 93739 AN: 151968 Hom.: 29206 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.617 AC: 93808 AN: 152088 Hom.: 29230 Cov.: 33 AF XY: 0.611 AC XY: 45444 AN XY: 74354

African (AFR) AF: 0.588 AC: 24379 AN: 41482

American (AMR) AF: 0.525 AC: 8021 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2113 AN: 3472

East Asian (EAS) AF: 0.423 AC: 2182 AN: 5164

South Asian (SAS) AF: 0.479 AC: 2308 AN: 4820

European-Finnish (FIN) AF: 0.639 AC: 6749 AN: 10560

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46070 AN: 67982

Other (OTH) AF: 0.619 AC: 1307 AN: 2112

Alfa AF: 0.629 Hom.: 5306

Bravo AF: 0.610

Asia WGS AF: 0.451 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.70
DANN	Benign	0.43
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs410569; hg19: chr6-160735746;