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 ENST00000414740.2(ENSG00000234261):​n.61-990A>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 ENST00000414740.2 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928354	XR_001743992.2	n.362-990A>G		intron_variant	Intron 4 of 4
LOC101928354	XR_007059472.1	n.284-990A>G		intron_variant	Intron 3 of 3
LOC101928354	XR_241980.4	n.224-990A>G		intron_variant	Intron 3 of 3
LOC101928354	XR_926516.3	n.187-990A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234261	ENST00000414740.2	n.61-990A>G		intron_variant	Intron 1 of 1	5
ENSG00000234261	ENST00000729738.1	n.288-990A>G		intron_variant	Intron 3 of 7
ENSG00000234261	ENST00000729739.1	n.224-990A>G		intron_variant	Intron 3 of 7

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 v4.3

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

Other links and lift over

dbSNP: rs7770731; hg19: chr6-14598820;