rs37973

Variant names:

• chr7-7968245-G-A
• rs37973
• ENST00000837984.1:n.296C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-7968245-G-A
• chr7-7968245-G-C
• chr7-7968245-G-T

Variant summary

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

The ENST00000837984.1(ENSG00000309036):​n.296C>T 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 0.628 in 152,128 control chromosomes in the GnomAD database, including 30,608 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 0.63 (30608 hom., cov: 33)
• Consequence: ENSG00000309036 ENST00000837984.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 64 publications found

Genes affected

ENSG00000309036 (HGNC:):

GLCCI1-DT (HGNC:40852): (GLCCI1 divergent transcript)

UMAD1 (HGNC:48955): (UBAP1-MVB12-associated (UMA) domain containing 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837984.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLCCI1-DT	NR_110018.1		n.209+299C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309036	ENST00000837984.1		n.296C>T		non_coding_transcript_exon	Exon 1 of 1
	GLCCI1-DT	ENST00000428660.1	TSL:4	n.132+1527C>T		intron	N/A
	GLCCI1-DT	ENST00000451066.2	TSL:5	n.56+299C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95411 AN: 152010 Hom.: 30581 Cov.: 33

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.628 AC: 95480 AN: 152128 Hom.: 30608 Cov.: 33 AF XY: 0.623 AC XY: 46354 AN XY: 74354

African (AFR) AF: 0.775 AC: 32161 AN: 41506

American (AMR) AF: 0.597 AC: 9129 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2192 AN: 3470

East Asian (EAS) AF: 0.525 AC: 2716 AN: 5174

South Asian (SAS) AF: 0.472 AC: 2277 AN: 4826

European-Finnish (FIN) AF: 0.579 AC: 6122 AN: 10578

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38872 AN: 67970

Other (OTH) AF: 0.647 AC: 1365 AN: 2110

Alfa AF: 0.592 Hom.: 69664

Bravo AF: 0.640

Asia WGS AF: 0.492 AC: 1714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.4
DANN	Benign	0.72
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs37973; hg19: chr7-8007876;