rs7742824

Variant names:

• chr6-44097574-G-A
• rs7742824

Your query was ambiguous. Multiple possible variants found:

• chr6-44097574-G-A
• chr6-44097574-G-T

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 0.261 in 151,316 control chromosomes in the GnomAD database, including 5,665 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 0.26 (5665 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 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: 0.261 AC: 39485 AN: 151200 Hom.: 5662 Cov.: 28

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.261 AC: 39509 AN: 151316 Hom.: 5665 Cov.: 28 AF XY: 0.259 AC XY: 19139 AN XY: 73928

African (AFR) AF: 0.381 AC: 15695 AN: 41166

American (AMR) AF: 0.212 AC: 3218 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 955 AN: 3466

East Asian (EAS) AF: 0.282 AC: 1439 AN: 5110

South Asian (SAS) AF: 0.168 AC: 808 AN: 4810

European-Finnish (FIN) AF: 0.222 AC: 2312 AN: 10424

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14203 AN: 67838

Other (OTH) AF: 0.263 AC: 549 AN: 2090

Alfa AF: 0.233 Hom.: 7990

Bravo AF: 0.270

Asia WGS AF: 0.220 AC: 767 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.66
DANN	Benign	0.39
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs7742824; hg19: chr6-44065311;