chr2-61692637-C-A

Variant names:

• chr2-61692637-C-A
• rs6705537
• ENST00000753764.1:n.265-9580G>T

Variant summary

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

The ENST00000753764.1(ENSG00000289410):​n.265-9580G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,174 control chromosomes in the GnomAD database, including 3,363 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 0.20 (3363 hom., cov: 33)
• Consequence: ENSG00000289410 ENST00000753764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 4 publications found

Genes affected

ENSG00000289410 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 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
ENSG00000289410	ENST00000753764.1	n.265-9580G>T		intron_variant	Intron 2 of 3
ENSG00000289410	ENST00000753765.1	n.348-9580G>T		intron_variant	Intron 2 of 2
ENSG00000289410	ENST00000753766.1	n.240-2866G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31146 AN: 152056 Hom.: 3361 Cov.: 33

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.00943

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.205 AC: 31165 AN: 152174 Hom.: 3363 Cov.: 33 AF XY: 0.200 AC XY: 14878 AN XY: 74404

African (AFR) AF: 0.269 AC: 11146 AN: 41506

American (AMR) AF: 0.141 AC: 2160 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 807 AN: 3472

East Asian (EAS) AF: 0.00945 AC: 49 AN: 5184

South Asian (SAS) AF: 0.128 AC: 618 AN: 4818

European-Finnish (FIN) AF: 0.177 AC: 1873 AN: 10586

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13746 AN: 67996

Other (OTH) AF: 0.197 AC: 417 AN: 2112

Alfa AF: 0.194 Hom.: 1126

Bravo AF: 0.205

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs6705537; hg19: chr2-61919772;