rs2317951

Variant names:

• chr1-54968975-G-A
• rs2317951
• ENST00000715514.1:c.1-17122G>A

Variant summary

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

The ENST00000715514.1(TMEM61):​c.1-17122G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,042 control chromosomes in the GnomAD database, including 7,717 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 0.31 (7717 hom., cov: 32)
• Consequence: TMEM61 ENST00000715514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 9 publications found

Genes affected

TMEM61 (HGNC:27296): (transmembrane protein 61) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

DHCR24-DT (HGNC:53969): (DHCR24 divergent transcript)

LOC124904184 (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 (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715514.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM61	ENST00000715514.1		c.1-17122G>A		intron	N/A	ENSP00000520459.1	A0AAQ5BIH8
	DHCR24-DT	ENST00000689429.1		n.325-4673G>A		intron	N/A
	DHCR24-DT	ENST00000715513.1		n.337-22861G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47817 AN: 151924 Hom.: 7722 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.315 AC: 47835 AN: 152042 Hom.: 7717 Cov.: 32 AF XY: 0.313 AC XY: 23232 AN XY: 74310

African (AFR) AF: 0.287 AC: 11919 AN: 41464

American (AMR) AF: 0.268 AC: 4085 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1407 AN: 3470

East Asian (EAS) AF: 0.132 AC: 684 AN: 5180

South Asian (SAS) AF: 0.295 AC: 1421 AN: 4816

European-Finnish (FIN) AF: 0.350 AC: 3699 AN: 10558

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23509 AN: 67980

Other (OTH) AF: 0.315 AC: 663 AN: 2108

Alfa AF: 0.333 Hom.: 27516

Bravo AF: 0.305

Asia WGS AF: 0.230 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.51
PhyloP100		-0.058

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2317951;

hg19: chr1-55434648;