1-54968770-T-G

Variant names:

• chr1-54968770-T-G
• rs2317948
• ENST00000715514.1:c.1-17327T>G

Variant summary

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

The ENST00000715514.1(TMEM61):​c.1-17327T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,122 control chromosomes in the GnomAD database, including 36,660 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 0.69 (36660 hom., cov: 33)
• Consequence: TMEM61 ENST00000715514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 7 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904184	XR_007066103.1	n.133-4878T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM61	ENST00000715514.1	c.1-17327T>G		intron_variant	Intron 1 of 2			ENSP00000520459.1
DHCR24-DT	ENST00000689429.1	n.325-4878T>G		intron_variant	Intron 1 of 1
DHCR24-DT	ENST00000715513.1	n.337-23066T>G		intron_variant	Intron 1 of 1
DHCR24-DT	ENST00000715515.1	n.408-4878T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105129 AN: 152002 Hom.: 36625 Cov.: 33

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.692 AC: 105227 AN: 152122 Hom.: 36660 Cov.: 33 AF XY: 0.693 AC XY: 51487 AN XY: 74348

African (AFR) AF: 0.741 AC: 30768 AN: 41518

American (AMR) AF: 0.761 AC: 11638 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2667 AN: 3472

East Asian (EAS) AF: 0.669 AC: 3445 AN: 5150

South Asian (SAS) AF: 0.603 AC: 2905 AN: 4820

European-Finnish (FIN) AF: 0.652 AC: 6891 AN: 10570

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44656 AN: 67988

Other (OTH) AF: 0.704 AC: 1486 AN: 2112

Alfa AF: 0.649 Hom.: 14606

Bravo AF: 0.703

Asia WGS AF: 0.630 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.21
DANN	Benign	0.32
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2317948; hg19: chr1-55434443;