10-7014054-C-G

Variant names:

• chr10-7014054-C-G
• rs4747385
• ENST00000664549.1:n.191-1398G>C

Variant summary

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

The NR_188183.1(LOC105376387):​n.191-1398G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,980 control chromosomes in the GnomAD database, including 17,973 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 0.48 (17973 hom., cov: 32)
• Consequence: LOC105376387 NR_188183.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 2 publications found

Genes affected

ENSG00000287277 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188183.1. 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
	LOC105376387	NR_188183.1		n.191-1398G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287277	ENST00000664549.1		n.191-1398G>C		intron	N/A
	ENSG00000287277	ENST00000666104.1		n.136-1398G>C		intron	N/A
	ENSG00000287277	ENST00000668409.1		n.154-1398G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72857 AN: 151862 Hom.: 17927 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.480 AC: 72966 AN: 151980 Hom.: 17973 Cov.: 32 AF XY: 0.485 AC XY: 35989 AN XY: 74276

African (AFR) AF: 0.579 AC: 23976 AN: 41436

American (AMR) AF: 0.537 AC: 8207 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3470

East Asian (EAS) AF: 0.562 AC: 2902 AN: 5168

South Asian (SAS) AF: 0.516 AC: 2481 AN: 4810

European-Finnish (FIN) AF: 0.416 AC: 4395 AN: 10560

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28342 AN: 67948

Other (OTH) AF: 0.449 AC: 945 AN: 2106

Alfa AF: 0.322 Hom.: 857

Bravo AF: 0.491

Asia WGS AF: 0.572 AC: 1988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.47
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs4747385; hg19: chr10-7056016;