rs7748279

Variant names:

• chr6-120917101-G-A
• rs7748279

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 0.146 in 152,078 control chromosomes in the GnomAD database, including 2,067 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 0.15 (2067 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 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: 0.146 AC: 22234 AN: 151960 Hom.: 2063 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.0879

Gnomad EAS AF: 0.0728

Gnomad SAS AF: 0.0862

Gnomad FIN AF: 0.0969

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.146 AC: 22251 AN: 152078 Hom.: 2067 Cov.: 32 AF XY: 0.143 AC XY: 10617 AN XY: 74370

African (AFR) AF: 0.266 AC: 11015 AN: 41450

American (AMR) AF: 0.0831 AC: 1269 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0879 AC: 305 AN: 3470

East Asian (EAS) AF: 0.0729 AC: 377 AN: 5168

South Asian (SAS) AF: 0.0854 AC: 411 AN: 4812

European-Finnish (FIN) AF: 0.0969 AC: 1027 AN: 10598

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.109 AC: 7426 AN: 67998

Other (OTH) AF: 0.127 AC: 268 AN: 2114

Alfa AF: 0.116 Hom.: 1993

Bravo AF: 0.150

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.73
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs7748279; hg19: chr6-121238247;