chr2-74769417-T-G

Position:

• chr2-74769417-T-G

Variant summary

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

The ENST00000674157.1(ENSG00000287687):​n.317+9047A>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 0.216 in 152,112 control chromosomes in the GnomAD database, including 3,779 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 0.22 (3779 hom., cov: 32)
• Consequence: ENST00000674157.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724482	XR_427046.4	n.293+9047A>C		intron_variant, non_coding_transcript_variant
LOC102724482	XR_940248.3	n.785+8555A>C		intron_variant, non_coding_transcript_variant
LOC102724482	XR_940249.3	n.315+9025A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000674157.1	n.317+9047A>C		intron_variant, non_coding_transcript_variant
	ENST00000690069.1	n.456+14567T>G		intron_variant, non_coding_transcript_variant
	ENST00000660620.1	n.279+9047A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32899 AN: 151994 Hom.: 3779 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.00577

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.216 AC: 32923 AN: 152112 Hom.: 3779 Cov.: 32 AF XY: 0.214 AC XY: 15904 AN XY: 74340

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.00598

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.189

Alfa AF: 0.222 Hom.: 855

Bravo AF: 0.208

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6740991; hg19: chr2-74996544;