rs903614

Variant names:

• chr8-118818441-A-C
• rs903614
• ENST00000625758.3:n.1320+54057A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-118818441-A-C
• chr8-118818441-A-G
• chr8-118818441-A-T

Variant summary

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

The ENST00000625758.3(SAMD12-AS1):​n.1320+54057A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,256 control chromosomes in the GnomAD database, including 1,266 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 0.12 (1266 hom., cov: 33)
• Consequence: SAMD12-AS1 ENST00000625758.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696
• Publications: 2 publications found

Genes affected

SAMD12-AS1 (HGNC:30937): (SAMD12 antisense RNA 1)

ENSG00000306504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.1320+54057A>C		intron_variant	Intron 6 of 7	5
SAMD12-AS1	ENST00000629661.1	n.496-39616A>C		intron_variant	Intron 4 of 4	5
SAMD12-AS1	ENST00000658340.1	n.900+54057A>C		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17693 AN: 152138 Hom.: 1261 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0972

Gnomad EAS AF: 0.0294

Gnomad SAS AF: 0.0821

Gnomad FIN AF: 0.0398

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0951

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.116 AC: 17714 AN: 152256 Hom.: 1266 Cov.: 33 AF XY: 0.111 AC XY: 8296 AN XY: 74446

African (AFR) AF: 0.205 AC: 8516 AN: 41554

American (AMR) AF: 0.0769 AC: 1175 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0972 AC: 337 AN: 3468

East Asian (EAS) AF: 0.0295 AC: 153 AN: 5184

South Asian (SAS) AF: 0.0820 AC: 395 AN: 4820

European-Finnish (FIN) AF: 0.0398 AC: 423 AN: 10618

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.0951 AC: 6470 AN: 68008

Other (OTH) AF: 0.102 AC: 216 AN: 2114

Alfa AF: 0.104 Hom.: 1899

Bravo AF: 0.122

Asia WGS AF: 0.0530 AC: 186 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.45
DANN	Benign	0.55
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs903614; hg19: chr8-119830680;