rs7581004

Positions:

• chr2-195009572-G-A

Variant summary

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

The ENST00000418387.1(ENSG00000235056):​n.147-4980C>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 0.303 in 151,192 control chromosomes in the GnomAD database, including 7,108 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 0.30 (7108 hom., cov: 33)
• Consequence: ENST00000418387.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376755	XR_007088699.1	n.265+49863C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000418387.1	n.147-4980C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45788 AN: 151074 Hom.: 7107 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.303 AC: 45812 AN: 151192 Hom.: 7108 Cov.: 33 AF XY: 0.303 AC XY: 22412 AN XY: 73846

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.292

Alfa AF: 0.281 Hom.: 5625

Bravo AF: 0.293

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7581004; hg19: chr2-195874296;