rs2974071

Variant names:

• chr5-86048537-A-G
• rs2974071
• ENST00000767533.1:n.135-39284A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000767533.1(ENSG00000299923):​n.135-39284A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,060 control chromosomes in the GnomAD database, including 5,280 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 0.23 (5280 hom., cov: 32)
• Consequence: ENSG00000299923 ENST00000767533.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 1 publications found

Genes affected

ENSG00000299923 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767533.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299923	ENST00000767533.1		n.135-39284A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35608 AN: 151944 Hom.: 5279 Cov.: 32

Gnomad AFR AF: 0.0621

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.234 AC: 35601 AN: 152060 Hom.: 5280 Cov.: 32 AF XY: 0.233 AC XY: 17347 AN XY: 74350

African (AFR) AF: 0.0620 AC: 2573 AN: 41522

American (AMR) AF: 0.231 AC: 3519 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1350 AN: 3470

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5178

South Asian (SAS) AF: 0.270 AC: 1303 AN: 4826

European-Finnish (FIN) AF: 0.307 AC: 3244 AN: 10568

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22593 AN: 67924

Other (OTH) AF: 0.251 AC: 529 AN: 2110

Alfa AF: 0.309 Hom.: 3980

Bravo AF: 0.219

Asia WGS AF: 0.126 AC: 436 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	2.7
DANN	Benign	0.92
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs2974071; hg19: chr5-85344355;