rs6707038

Positions:

• chr2-237924622-G-A
• chr2-237924622-G-T

Variant summary

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

The ENST00000686788.1(ENSG00000288857):​n.260-900C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,066 control chromosomes in the GnomAD database, including 28,547 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 0.61 (28547 hom., cov: 33)
• Consequence: ENST00000686788.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373960	XR_924046.3	n.75-900C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000686788.1	n.260-900C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92331 AN: 151948 Hom.: 28504 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.608 AC: 92433 AN: 152066 Hom.: 28547 Cov.: 33 AF XY: 0.620 AC XY: 46063 AN XY: 74344

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.611

Alfa AF: 0.560 Hom.: 30225

Bravo AF: 0.598

Asia WGS AF: 0.628 AC: 2185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.73
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6707038; hg19: chr2-238833264;