rs7770731

Variant names:

• chr6-14598589-T-C
• rs7770731
• ENST00000414740.2:n.61-990A>G

Variant summary

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

The ENST00000729738.1(ENSG00000234261):​n.288-990A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,110 control chromosomes in the GnomAD database, including 7,233 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 0.28 (7233 hom., cov: 32)
• Consequence: ENSG00000234261 ENST00000729738.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 8 publications found

Genes affected

ENSG00000234261 (HGNC:):

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 = 0.458 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729738.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234261	ENST00000414740.2	TSL:5	n.61-990A>G		intron	N/A
	ENSG00000234261	ENST00000729738.1		n.288-990A>G		intron	N/A
	ENSG00000234261	ENST00000729739.1		n.224-990A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42679 AN: 151992 Hom.: 7219 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.281 AC: 42732 AN: 152110 Hom.: 7233 Cov.: 32 AF XY: 0.280 AC XY: 20816 AN XY: 74372

African (AFR) AF: 0.464 AC: 19230 AN: 41482

American (AMR) AF: 0.189 AC: 2894 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 682 AN: 3468

East Asian (EAS) AF: 0.181 AC: 937 AN: 5168

South Asian (SAS) AF: 0.427 AC: 2055 AN: 4818

European-Finnish (FIN) AF: 0.179 AC: 1893 AN: 10574

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14275 AN: 67988

Other (OTH) AF: 0.264 AC: 559 AN: 2116

Alfa AF: 0.238 Hom.: 13501

Bravo AF: 0.283

Asia WGS AF: 0.338 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.62
PhyloP100		-0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7770731;

hg19: chr6-14598820;