rs2049314

Positions:

• chr7-91834820-C-T

Variant summary

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

The variant allele was found at a frequency of 0.341 in 152,058 control chromosomes in the GnomAD database, including 9,207 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 0.34 (9207 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.91834820C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTERF1	ENST00000454222.5	n.94-7340G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51904 AN: 151940 Hom.: 9206 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.341 AC: 51923 AN: 152058 Hom.: 9207 Cov.: 32 AF XY: 0.339 AC XY: 25190 AN XY: 74316

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.377

Alfa AF: 0.379 Hom.: 6330

Bravo AF: 0.338

Asia WGS AF: 0.297 AC: 1032 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.099
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: rs2049314; hg19: chr7-91464134;