chr7-121305163-A-G

Variant names:

• chr7-121305163-A-G
• rs1547960
• ENST00000657332.1:n.2870T>C

Variant summary

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

The ENST00000657332.1(ENSG00000287554):​n.2870T>C 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 0.424 in 151,910 control chromosomes in the GnomAD database, including 14,529 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 0.42 (14529 hom., cov: 32)
• Consequence: ENSG00000287554 ENST00000657332.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 8 publications found

Genes affected

ENSG00000287554 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287554	ENST00000657332.1	n.2870T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64349 AN: 151792 Hom.: 14512 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.424 AC: 64417 AN: 151910 Hom.: 14529 Cov.: 32 AF XY: 0.420 AC XY: 31190 AN XY: 74238

African (AFR) AF: 0.568 AC: 23489 AN: 41390

American (AMR) AF: 0.362 AC: 5530 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1532 AN: 3468

East Asian (EAS) AF: 0.417 AC: 2150 AN: 5156

South Asian (SAS) AF: 0.568 AC: 2732 AN: 4808

European-Finnish (FIN) AF: 0.286 AC: 3024 AN: 10570

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24694 AN: 67942

Other (OTH) AF: 0.437 AC: 920 AN: 2106

Alfa AF: 0.392 Hom.: 6424

Bravo AF: 0.432

Asia WGS AF: 0.515 AC: 1789 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1547960; hg19: chr7-120945217;