rs6708544

Variant names:

• chr2-174739466-G-A
• rs6708544
• ENST00000442996.1:n.321+9642G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-174739466-G-A
• chr2-174739466-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000442996.1(ENSG00000236449):​n.321+9642G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,944 control chromosomes in the GnomAD database, including 9,560 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 0.32 (9560 hom., cov: 31)
• Consequence: ENSG00000236449 ENST00000442996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

Genes affected

ENSG00000236449 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 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
ENSG00000236449	ENST00000442996.1	n.321+9642G>A		intron_variant	Intron 3 of 3	1

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48851 AN: 151824 Hom.: 9567 Cov.: 31

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.321 AC: 48844 AN: 151944 Hom.: 9560 Cov.: 31 AF XY: 0.332 AC XY: 24645 AN XY: 74256

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.299

Alfa AF: 0.348 Hom.: 4532

Bravo AF: 0.308

Asia WGS AF: 0.496 AC: 1728 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	1.5
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6708544; hg19: chr2-175604194;