rs205611

chr2-74744954-A-G

Variant summary

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

The ENST00000674157.1(ENSG00000287687):n.318-3301T>C 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 0.149 in 152,176 control chromosomes in the GnomAD database, including 1,983 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 0.15 (1983 hom., cov: 32)
• Consequence: ENST00000674157.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724497	XR_427047.5	n.138-9608A>G		intron_variant, non_coding_transcript_variant
LOC102724497	XR_001739541.2	n.515-9608A>G		intron_variant, non_coding_transcript_variant
LOC102724497	XR_001739542.2	n.952-9608A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000674157.1	n.318-3301T>C		intron_variant, non_coding_transcript_variant
	ENST00000690069.1	n.168-9608A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22591 AN: 152058 Hom.: 1982 Cov.: 32

Gnomad AFR AF: 0.0871

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0693

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.149 AC: 22603 AN: 152176 Hom.: 1983 Cov.: 32 AF XY: 0.147 AC XY: 10963 AN XY: 74398

Gnomad4 AFR AF: 0.0871

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0692

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.143

Alfa AF: 0.180 Hom.: 5558

Bravo AF: 0.134

Asia WGS AF: 0.0440 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	8.6
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs205611; hg19: chr2-74972081;