rs2880072

Variant names:

• chr6-159404417-G-A
• rs2880072
• ENST00000753126.1:n.202-28543C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-159404417-G-A
• chr6-159404417-G-C
• chr6-159404417-G-T

Variant summary

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

The ENST00000753126.1(ENSG00000231178):​n.202-28543C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,860 control chromosomes in the GnomAD database, including 19,050 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 0.49 (19050 hom., cov: 31)
• Consequence: ENSG00000231178 ENST00000753126.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 3 publications found

Genes affected

ENSG00000231178 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 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
ENSG00000231178	ENST00000753126.1	n.202-28543C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73627 AN: 151740 Hom.: 19020 Cov.: 31

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.485 AC: 73698 AN: 151860 Hom.: 19050 Cov.: 31 AF XY: 0.485 AC XY: 35980 AN XY: 74192

African (AFR) AF: 0.670 AC: 27758 AN: 41424

American (AMR) AF: 0.386 AC: 5891 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1540 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2712 AN: 5150

South Asian (SAS) AF: 0.556 AC: 2680 AN: 4818

European-Finnish (FIN) AF: 0.385 AC: 4051 AN: 10520

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27707 AN: 67912

Other (OTH) AF: 0.459 AC: 971 AN: 2114

Alfa AF: 0.457 Hom.: 2780

Bravo AF: 0.488

Asia WGS AF: 0.540 AC: 1881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.37
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2880072; hg19: chr6-159825449;