8-7418812-G-A

Variant names:

• chr8-7418812-G-A
• rs2740083

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.202 in 137,212 control chromosomes in the GnomAD database, including 127 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 0.20 (127 hom., cov: 48)
• Consequence: HSPD1P3 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 1 publications found

Genes affected

HSPD1P3 (HGNC:5264): (heat shock protein family D (Hsp60) member 1 pseudogene 3)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS2: High Homozygotes in GnomAd4 at 127 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533477.1. 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
	HSPD1P3	ENST00000533477.1	TSL:6	n.-179G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.202 AC: 27741 AN: 137110 Hom.: 128 Cov.: 48

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.202 AC: 27742 AN: 137212 Hom.: 127 Cov.: 48 AF XY: 0.200 AC XY: 13430 AN XY: 67194

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.112 AC: 4302 AN: 38288

American (AMR) AF: 0.160 AC: 2241 AN: 13976

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 752 AN: 3094

East Asian (EAS) AF: 0.320 AC: 1483 AN: 4632

South Asian (SAS) AF: 0.225 AC: 971 AN: 4322

European-Finnish (FIN) AF: 0.223 AC: 2143 AN: 9596

Middle Eastern (MID) AF: 0.186 AC: 48 AN: 258

European-Non Finnish (NFE) AF: 0.252 AC: 15214 AN: 60340

Other (OTH) AF: 0.202 AC: 384 AN: 1900

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.122 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.37
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2740083; hg19: chr8-7276334; COSMIC: COSV58939901;