chr8-66535418-G-T

Position:

• chr8-66535418-G-T

Variant summary

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

The XR_007060952.1(LOC124901955):​n.207+6541C>A 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 0.0909 in 152,224 control chromosomes in the GnomAD database, including 1,536 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 0.091 (1536 hom., cov: 31)
• Consequence: LOC124901955 XR_007060952.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

LOC124901955 (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 (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901955	XR_007060952.1	n.207+6541C>A		intron_variant, non_coding_transcript_variant
LOC124901955	XR_007060951.1	n.207+6541C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0907 AC: 13798 AN: 152106 Hom.: 1532 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0716

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.0131

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0909 AC: 13836 AN: 152224 Hom.: 1536 Cov.: 31 AF XY: 0.0899 AC XY: 6691 AN XY: 74436

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.0718

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.0265

Gnomad4 FIN AF: 0.0131

Gnomad4 NFE AF: 0.0105

Gnomad4 OTH AF: 0.0738

Alfa AF: 0.0236 Hom.: 404

Bravo AF: 0.103

Asia WGS AF: 0.0750 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.057
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7008801; hg19: chr8-67447653;