rs1025195

Variant names:

• chr7-136243667-C-A
• rs1025195
• ENST00000659747.1:n.1748C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-136243667-C-A
• chr7-136243667-C-G
• chr7-136243667-C-T

Variant summary

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

The ENST00000659747.1(ENSG00000232053):​n.1748C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 152,032 control chromosomes in the GnomAD database, including 35,391 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 0.68 (35391 hom., cov: 32)
• Consequence: ENSG00000232053 ENST00000659747.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 1 publications found

Genes affected

ENSG00000232053 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375523	NR_187952.1	n.1630C>A		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105375523	NR_187953.1	n.1832C>A		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105375523	NR_187954.1	n.1938C>A		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232053	ENST00000659747.1	n.1748C>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000232053	ENST00000720839.1	n.2067C>A		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000232053	ENST00000720840.1	n.1897C>A		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103235 AN: 151914 Hom.: 35361 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.680 AC: 103318 AN: 152032 Hom.: 35391 Cov.: 32 AF XY: 0.678 AC XY: 50395 AN XY: 74280

African (AFR) AF: 0.689 AC: 28602 AN: 41490

American (AMR) AF: 0.725 AC: 11077 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2538 AN: 3472

East Asian (EAS) AF: 0.872 AC: 4500 AN: 5160

South Asian (SAS) AF: 0.748 AC: 3606 AN: 4818

European-Finnish (FIN) AF: 0.552 AC: 5815 AN: 10542

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44879 AN: 67954

Other (OTH) AF: 0.703 AC: 1479 AN: 2104

Alfa AF: 0.674 Hom.: 18791

Bravo AF: 0.695

Asia WGS AF: 0.825 AC: 2866 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.057
DANN	Benign	0.52
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1025195; hg19: chr7-135928415;