rs6944937

Variant names:

• chr7-85989176-T-C
• rs6944937
• ENST00000757672.1:n.224-22575A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000757672.1(ENSG00000298738):​n.224-22575A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,144 control chromosomes in the GnomAD database, including 3,340 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 0.20 (3340 hom., cov: 32)
• Consequence: ENSG00000298738 ENST00000757672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 2 publications found

Genes affected

ENSG00000298738 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757672.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298738	ENST00000757672.1		n.224-22575A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30939 AN: 152026 Hom.: 3338 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.203 AC: 30942 AN: 152144 Hom.: 3340 Cov.: 32 AF XY: 0.202 AC XY: 15018 AN XY: 74372

African (AFR) AF: 0.133 AC: 5533 AN: 41532

American (AMR) AF: 0.196 AC: 2987 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3472

East Asian (EAS) AF: 0.177 AC: 915 AN: 5160

South Asian (SAS) AF: 0.201 AC: 969 AN: 4830

European-Finnish (FIN) AF: 0.229 AC: 2421 AN: 10582

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16400 AN: 67986

Other (OTH) AF: 0.225 AC: 475 AN: 2112

Alfa AF: 0.232 Hom.: 17774

Bravo AF: 0.202

Asia WGS AF: 0.188 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.46
DANN	Benign	0.90
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs6944937; hg19: chr7-85618492;