chr6-105635397-G-A

Variant names:

• chr6-105635397-G-A
• rs7754740

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 0.097 in 152,180 control chromosomes in the GnomAD database, including 1,315 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 0.097 (1315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0969 AC: 14732 AN: 152060 Hom.: 1306 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0853

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0905

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0219

Gnomad OTH AF: 0.0901

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

GnomAD4 genome AF: 0.0970 AC: 14767 AN: 152180 Hom.: 1315 Cov.: 32 AF XY: 0.101 AC XY: 7503 AN XY: 74394

African (AFR) AF: 0.209 AC: 8654 AN: 41498

American (AMR) AF: 0.0858 AC: 1311 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1556 AN: 5162

South Asian (SAS) AF: 0.101 AC: 488 AN: 4828

European-Finnish (FIN) AF: 0.0905 AC: 959 AN: 10602

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0219 AC: 1489 AN: 68020

Other (OTH) AF: 0.0939 AC: 198 AN: 2108

Alfa AF: 0.0110 Hom.: 3

Bravo AF: 0.104

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.19
DANN	Benign	0.19
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs7754740; hg19: chr6-106083272;