chr6-4558976-T-C

Position:

• chr6-4558976-T-C

Variant summary

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

The ENST00000642310.1(ENSG00000285424):​n.313+22663A>G 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 0.157 in 152,060 control chromosomes in the GnomAD database, including 1,950 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 0.16 (1950 hom., cov: 32)
• Consequence: ENST00000642310.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374894	XR_007059418.1	n.287+22663A>G		intron_variant, non_coding_transcript_variant
LOC105374894	XR_001743940.2	n.287+22663A>G		intron_variant, non_coding_transcript_variant
LOC105374894	XR_007059417.1	n.287+22663A>G		intron_variant, non_coding_transcript_variant
LOC105374894	XR_926409.3	n.287+22663A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000642310.1	n.313+22663A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23894 AN: 151944 Hom.: 1949 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0784

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.157 AC: 23916 AN: 152060 Hom.: 1950 Cov.: 32 AF XY: 0.153 AC XY: 11381 AN XY: 74310

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.0793

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.181

Alfa AF: 0.160 Hom.: 425

Bravo AF: 0.159

Asia WGS AF: 0.122 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs84996; hg19: chr6-4559210;